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- PDB-5o58: Structure of the inactive T.maritima PDE (TM1595) D80N D154N muta... -

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Basic information

Entry
Database: PDB / ID: 5o58
TitleStructure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApG
Components
  • RNA (5'-R(P*AP*G)-3')
  • phosphodiesterase TM1595
KeywordsHYDROLASE / phosphodiesterase
Function / homology
Function and homology information


nucleic acid binding / nucleotide binding / metal ion binding
Similarity search - Function
: / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / RNA / Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWitte, G. / Drexler, D. / Mueller, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation3717/3-1 Germany
German Research FoundationGRK1721 Germany
CitationJournal: Structure / Year: 2017
Title: Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.
Authors: Drexler, D.J. / Muller, M. / Rojas-Cordova, C.A. / Bandera, A.M. / Witte, G.
History
DepositionJun 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 6, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.5Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phosphodiesterase TM1595
B: RNA (5'-R(P*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,98727
Polymers38,4982
Non-polymers1,48925
Water5,026279
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering, static lightscattering= TmPDE is dimeric in solution, no detectable monomer fraction, SAXS, SAXS scattering curve is only compatible with the dimeric assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint36 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.370, 88.340, 124.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

21A-767-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein phosphodiesterase TM1595


Mass: 37868.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: TM_1595 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1T1
#2: RNA chain RNA (5'-R(P*AP*G)-3')


Mass: 629.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 304 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% (w/v) 2-propanol 0.1M sodium acetate pH4.6 0.2M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.1999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1999 Å / Relative weight: 1
ReflectionResolution: 1.55→62 Å / Num. obs: 106913 / % possible obs: 98.4 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rrim(I) all: 0.037 / Net I/σ(I): 19.2
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.87 / Num. unique obs: 7687 / CC1/2: 0.75 / Rrim(I) all: 0.828 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O4Z

5o4z


Resolution: 1.55→50.326 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1835 5384 5.04 %
Rwork0.1579 --
obs0.1592 106907 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→50.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 46 94 279 2987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062808
X-RAY DIFFRACTIONf_angle_d0.8113781
X-RAY DIFFRACTIONf_dihedral_angle_d5.0812257
X-RAY DIFFRACTIONf_chiral_restr0.058413
X-RAY DIFFRACTIONf_plane_restr0.005478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.56760.35741690.3263282X-RAY DIFFRACTION93
1.5676-1.5860.30811920.2943235X-RAY DIFFRACTION97
1.586-1.60540.30751690.29273389X-RAY DIFFRACTION97
1.6054-1.62570.28531630.28173329X-RAY DIFFRACTION97
1.6257-1.64710.31391620.27153362X-RAY DIFFRACTION98
1.6471-1.66960.31391950.24913351X-RAY DIFFRACTION97
1.6696-1.69350.23622000.24343327X-RAY DIFFRACTION98
1.6935-1.71880.24891810.22973386X-RAY DIFFRACTION97
1.7188-1.74560.23731380.22863389X-RAY DIFFRACTION98
1.7456-1.77430.25152260.20973347X-RAY DIFFRACTION98
1.7743-1.80480.22391730.19073365X-RAY DIFFRACTION98
1.8048-1.83770.21131820.18253364X-RAY DIFFRACTION99
1.8377-1.8730.18462130.18153371X-RAY DIFFRACTION98
1.873-1.91120.18311570.1643409X-RAY DIFFRACTION98
1.9112-1.95280.20581490.15953459X-RAY DIFFRACTION99
1.9528-1.99820.20981960.15523363X-RAY DIFFRACTION99
1.9982-2.04820.16282060.15073335X-RAY DIFFRACTION99
2.0482-2.10360.16032010.14623446X-RAY DIFFRACTION99
2.1036-2.16550.16711800.14773420X-RAY DIFFRACTION99
2.1655-2.23540.17471580.14853391X-RAY DIFFRACTION99
2.2354-2.31530.15521710.1523417X-RAY DIFFRACTION99
2.3153-2.4080.16911920.14823404X-RAY DIFFRACTION99
2.408-2.51760.19621710.1463386X-RAY DIFFRACTION99
2.5176-2.65030.17561590.15343435X-RAY DIFFRACTION99
2.6503-2.81630.18191540.14273492X-RAY DIFFRACTION99
2.8163-3.03380.16671900.14343392X-RAY DIFFRACTION100
3.0338-3.3390.17741910.14123424X-RAY DIFFRACTION99
3.339-3.8220.15331860.13853395X-RAY DIFFRACTION99
3.822-4.81470.18111840.13173430X-RAY DIFFRACTION100
4.8147-50.35250.17471760.17043428X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2466-0.04260.04780.06890.07250.30460.1611-0.19740.04180.1957-0.155-0.01450.00570.037400.302-0.05740.01490.26390.00610.2571-11.081-24.0411-6.2314
20.3895-0.0266-0.0220.3220.06090.57630.13480.01360.08730.166-0.08840.1133-0.1512-0.081500.2649-0.01620.040.2535-0.0040.2645-17.0012-16.1368-12.17
30.53320.2663-0.12440.5515-0.05180.59980.0489-0.0652-0.02910.0779-0.0602-0.04690.06760.0264-00.2383-0.03250.00250.2389-0.00550.2267-5.2646-20.3561-14.5587
40.4793-0.0992-0.05610.4664-0.05790.9224-0.0621-0.02690.1387-0.07780.01690.0979-0.2024-0.064400.25660.0142-0.00140.2297-0.00340.2288-1.93993.7102-23.7597
50.07280.11440.0830.17120.11970.1883-0.09230.0043-0.1472-0.08640.01260.0549-0.1760.0264-0.00010.24320.0052-0.00440.2481-0.01830.25392.29861.4855-22.9936
60.16850.09250.13710.06590.03840.1180.0377-0.0949-0.08660.1673-0.04760.0794-0.14790.0186-0.00020.256-0.00730.01260.2419-0.04480.24782.43013.1977-12.7646
70.48980.06830.14280.1612-0.24710.47470.1028-0.0821-0.05890.3144-0.0999-0.08220.07350.068100.2861-0.0185-0.01840.25950.00090.265112.9879-0.4823-10.4707
80.03490.0331-0.00530.025-0.00360.00590.03890.199-0.0173-0.34640.2882-0.10150.0370.06320.00080.3896-0.0726-0.00320.3026-0.02830.32742.3262-8.1847-14.9772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 176 )
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 228 )
5X-RAY DIFFRACTION5chain 'A' and (resid 229 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 268 )
7X-RAY DIFFRACTION7chain 'A' and (resid 269 through 320 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 2 )

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